Bioinformatics for Proteomics

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bioinformatics for proteomics

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Identification

Database Generation 10 Topics

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Database Choice

Database Choice (continued)

About Sample Contamination

Adding Trypsin Protein Sequence

Non-standard Databases (advanced)

Peak List Generation 10 Topics

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Peak List Generation

Raw Files Conversion – ThermoRawFileParserGUI

Raw Files Conversion – ThermoRawFileParserGUI (continued)

Raw Files Conversion – ThermoRawFileParserGUI (continued)

Raw Files Conversion – ProteoWizard

Advanced: Signal Processing

Resources & Tools

Peptide to Spectrum Matching 17 Topics

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Peptide to Spectrum Matching

Search Settings

Database Details

Choose the enzyme – Exercise 1.3d

Mass tolerance – Exercise 1.3e

Find Modification

Modification Details – Exercise 1.3h

Resources & Tools

Browsing Identification Results 44 Topics

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Peptide and Protein Validation 16 Topics

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Peptide and Protein Validation

Validation Threshold

Current Threshold Settings

PSM – Exercise 1.5g

New Validation Settings – Exercise 1.5h

Protein Group Validation Quality

Resources & Tools

PTM Analysis 21 Topics

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De Novo Peptide Identification 16 Topics

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Resources & Tools

De Novo Sequencing

Specify Modifications

Functional Analysis

Functional Analysis 15 Topics

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Resources & Tools

Functional Analysis

*** PART A. PROTEIN INFORMATION ***

*** PART B. PATHWAYS ***

*** PART C. GO ANALYSIS ***

*** PART D. 3D STRUCTURES ***

Data Sharing

Data Sharing – Introduction 2 Topics

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Submit 10 Topics

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Resources & Tools

Submitting to Online Repositories

The ProteomeXchange Submission Tool

Annotate the Result Files

Lab Head Details

Browse 6 Topics

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Resources & Tools

Browsing Online Repositories

Pride Inspector

Reprocess 6 Topics

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Reprocessing Public Experiments

Reprocess Assay 1644

Value of Reshake

Quantification

Quantification – Introduction 2 Topics

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Peptide and Protein Quantification

Spectrum Counting 5 Topics

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Resources & Tools

Spectrum Counting Quantification

Spectrum Counting in PeptideShaker

Reporter Ions 14 Topics

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Resources & Tools

Reporter Ion Based Quantification

Interpretation Strategy

Start Searching

Converting Intensities into Peptide & Protein Relative Abundances

Start Quantifying

MS1 Quantification (in preparation)

Targeted Quantification (in preparation)

Statistical Analysis 21 Topics

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Resources & Tools

Statistical Analysis

File Import – Exercise 4.5a

Filtering and Rearranging Columns – Exercise 4.5b

Filtering out Proteins with Missing Values – Exercise 4.5d

Normalization – Exercise 4.5g

Subtract – Exercise 4.5h

Student’s t-test – Exercise 4.5i

Value imputation

Principal Component Analysis (PCA) – Exercise 4.5m

Hierarchical Clustering – Exercise 4.5n

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This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 License.

Harald Barsnes (harald.barsnes@uib.no), Marc Vaudel (marc.vaudel@uib.no) and Lennart Martens
(lennart.martens@vib-ugent.be)

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